(Q51629171)

3 July 2018

title

New heuristic methods for joint species delimitation and species tree inference. (English)

1 reference

3 July 2018

author

Brian C O'Meara

series ordinal

1

1 reference

http://europepmc.org/abstract/MED/20525620

8 April 2018

publication date

10 November 2009

1 reference

3 July 2018

published in

Systematic Biology

1 reference

3 July 2018

volume

59

1 reference

3 July 2018

issue

1

1 reference

3 July 2018

page(s)

59-73

1 reference

3 July 2018

Comparison of species tree methods for reconstructing the phylogeny of bearded manakins (Aves: Pipridae, Manacus) from multilocus sequence data

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3 July 2018

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3 July 2018

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Delimiting species in recent radiations

3 July 2018

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Delimiting species without monophyletic gene trees

3 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Species concepts and species delimitation

3 July 2018

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https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions

3 July 2018

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Estimating species phylogeny from gene-tree probabilities despite incomplete lineage sorting: an example from Melanoplus grasshoppers

3 July 2018

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High-resolution species trees without concatenation

3 July 2018

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A step toward barcoding life: a model-based, decision-theoretic method to assign genes to preexisting species groups

3 July 2018

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The latitudinal gradient in recent speciation and extinction rates of birds and mammals

3 July 2018

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Inferring angiosperm phylogeny from EST data with widespread gene duplication

3 July 2018

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Sequence-based species delimitation for the DNA taxonomy of undescribed insects

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Discordance of species trees with their most likely gene trees.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Assignment methods: matching biological questions with appropriate techniques

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Inferring phylogeny despite incomplete lineage sorting

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

A Likelihood Framework for Inferring the Evolution of Geographic Range on Phylogenetic Trees

3 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

3 July 2018

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

A likelihood ratio test for species membership based on DNA sequence data

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

RAxML-III: a fast program for maximum likelihood-based inference of large phylogenetic trees

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Bayes estimation of species divergence times and ancestral population sizes using DNA sequences from multiple loci

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Biological identifications through DNA barcodes

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Approximate Bayesian computation in population genetics

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Likelihood and Bayes estimation of ancestral population sizes in hominoids using data from multiple loci

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Inferring the history of speciation from multilocus DNA sequence data: the case of Drosophila pseudoobscura and close relatives

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Generating samples under a Wright-Fisher neutral model of genetic variation

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach

3 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

3 July 2018

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Distinguishing migration from isolation: a Markov chain Monte Carlo approach

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Maximum likelihood estimation of a migration matrix and effective population sizes in n subpopulations by using a coalescent approach

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Maximum-likelihood estimation of migration rates and effective population numbers in two populations using a coalescent approach

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Inferring species trees from gene trees: a phylogenetic analysis of the Elapidae (Serpentes) based on the amino acid sequences of venom proteins

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Gene flow and natural selection in the origin of Drosophila pseudoobscura and close relatives

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Links between maximum likelihood and maximum parsimony under a simple model of site substitution

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Inferring coalescence times from DNA sequence data

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Evolutionary relationship of DNA sequences in finite populations

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Mitochondrial DNA differentiation during the speciation process in Peromyscus

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Distinguishing Homologous from Analogous Proteins

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Relationships between gene trees and species trees

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Progressive sequence alignment as a prerequisite to correct phylogenetic trees

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

A cladistic measure of gene flow inferred from the phylogenies of alleles

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Gene trees, species trees and the segregation of ancestral alleles

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

CLUSTAL V: improved software for multiple sequence alignment

3 July 2018

2 references

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

3 July 2018

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

Estimation of levels of gene flow from DNA sequence data

21 January 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Incomplete lineage sorting: consistent phylogeny estimation from multiple loci.

3 July 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

STEM: species tree estimation using maximum likelihood for gene trees under coalescence.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

A genealogical approach to quantifying lineage divergence.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Inferring species membership using DNA sequences with back-propagation neural networks

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Species delimitation and phylogenetic relationships in Lactarius section Deliciosi in Europe

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Testing for different rates of continuous trait evolution using likelihood

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Gene tree distributions under the coalescent process

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

A multilocus genealogical approach to phylogenetic species recognition in the model eukaryote Neurospora.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Gene tree parsimony vs uninode coding for phylogenetic reconstruction

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

The causes of phylogenetic conflict in a classic Drosophila species group.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Mathematical consequences of the genealogical species concept.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Is the Felsenstein zone a fly trap?

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

A simple algorithm to infer gene duplication and speciation events on a gene tree.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

Distributions of cherries for two models of trees.

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

PHYLOGENETIC ANALYSIS: MODELS AND ESTIMATION PROCEDURES

14 August 2018

1 reference

https://eutils.ncbi.nlm.nih.gov/entrez/eutils/elink.fcgi?dbfrom=pmc&linkname=pmc_refs_pubmed&retmode=json&id=5841455

A new look at the statistical model identification

29 September 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

Combining Trees as a Way of Combining Data Sets for Phylogenetic Inference, and the Desirability of Combining Gene Trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

Species-Level Paraphyly and Polyphyly: Frequency, Causes, and Consequences, with Insights from Animal Mitochondrial DNA

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

Phylogenetic inference based on matrix representation of trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

Further analysts of the data by akaike' s information criterion and the finite corrections

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

Links between maximum likelihood and maximum parsimony under a simple model of site substitution

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

Analogs & duals of the MAST problem for sequences & trees

21 January 2018

1 reference

https://api.crossref.org/works/10.1093%2FSYSBIO%2FSYP077

21 January 2018

Identifiers

DOI

10.1093/SYSBIO/SYP077

1 reference

3 July 2018

PMCID

5841455

1 reference

3 July 2018

PubMed ID

20525620

1 reference

3 July 2018